The Sand ninja fight against time to treat Kankuro. Even the Sand’s poison expert, Granny Chiyo, is baffled. The only hope lies with the reinforcements sent by Tsunade.

Teams Kakashi and Guy reach the Akatsuki hideout. They hurry to infiltrate but are thwarted by a five-seal barrier. The only way to break the barrier is to remove all five seals at once.

Although stung with poison herself, Granny Chiyo uses the last of the antidote on Sakura. Mocking the tender scene between Granny Chiyo and Sakura, Sasori attempts to end Granny Chiyo's life.

Naruto, Choji and Shikamaru attempt to capture and interrogate Sai, but Sai withdraws after insulting Naruto. Shortly afterward, Ino appears. Concerned that the demon fox could fall into Akatsuki hands, the village elders challenge Tsunade's plan to send Naruto out of the village without the still bedridden Kakashi. Tsunade promises to protect Konoha with her own life if Naruto is captured, but is still forced to compromise with Danzo by adding Sai to Team Kakashi. She also temporarily replaces Kakashi with ANBU member Yamato and warns him to keep an eye on Sai. Naruto and Sakura finally meet their new team members, and Naruto is immediately angered upon Sai's appearance.

As Team Kakashi continues their search for Sasuke, Naruto suddenly collapses due to his previous fight with Orochimaru. As Naruto wakes up, Sai begins to reveal more about his brother, but Orochimaru suddenly attacks them. Sakura and Yamato come to Naruto's aid against Orochimaru, while Sai continues the search. Just as Sai finds Sasuke, Yamato finds Sai's bingo book with Sasuke listed as a target for assassination.

The temple monks explain that the tombs hold the loyal bodyguards of Fire Country's feudal lord. Naruto observes Sora sparring with other monks and becomes offended upon realizing he is holding back. Naruto challenges Sora, but just as the matter is about to get serious, another monk stops him. Naruto realizes Sora is despised by the other monks as he was himself and wishes to befriend him. Naruto visits Sora again and observes him practicing his wind jutsu in earnest, hoping to get strong enough to avenge his father. They later return to the temple to receive news that another tomb has been robbed.

Konoha's ninja fight off the revived zombie members of the Kohaku clan. The four Guardian Ninjas, Seito, Tōu, Nauma and Kitane, are also revived. Asuma realizes that they are planning to use Limelight, a jutsu in which the four create a lightning blast powerful enough to destroy Konoha. Asuma sends Sakura and Yamato after the other three while he remains behind to battle Kitane, but Fuen tackles Sakura and Fudo fights Yamato. Meanwhile, Naruto catches up to Sora, but Sora runs off in search of Furido. Naruto tries to pursue him, but is assailed by Fuuka. Soon after, Sora reaches Furido, who admits that he had planned to destroy Konoha.

The second stage of Naruto's training continues, while Tsunade sends out twenty teams composed of four ninja each to deal with the Akatsuki members in the Fire Country. Shikamaru leaves with Asuma, Izumo and Kotetsu, whereas Ino and Choji leave with Raido and Aoba. After putting in considerable effort, Naruto clears the second stage of his training, but collapses from hunger and exhaustion almost immediately afterward.

With careful planning, the group manages to find and trap Hidan and Kakuzu. However, things seem to be going a bit too smoothly.

Guren is rendered unconscious and relives her past as Naruto is caught in an illusion about Sasuke. After Kakashi finds him, Teams Kakashi and Kurenai conclude the mist around them causes Genjutsu courtesy of the Three-Tails. After Guren wakes up, Yūkimaru suffers another fever and passes out. Tsunade hears of the Three-Tails and assmbles Shizune, Ino, Tenten and Lee to go and seal it before the Akatsuki do. Naruto and Sakura talk about the home that people should return to before Naruto heads off to find Yūkimaru.

Yukimaru informs Kakashi and the others to Naruto and Guren's whereabouts and they attempt to free them with Yukimaru's help. Kiba, Tenten and Lee once again battle Kihou, Kigiri and Nurari after gaining more power from Kabuto. Naruto and Guren continue to search for a way out, coming across human-sized Sanbi-like creatures and illusions. Will Naruto and Guren ever find a way out?

The second member of Sasuke's team is revealed to be a woman named Karin. After Sasuke and Suigetsu arrive at the Southern Hideout, Sasuke requests that Karin comes with them. Despite her hesitations and quarrels with Suigetsu, Karin ultimately accepts after remembering her very first encounter with Sasuke. Sasuke orders Suigetsu to release the prisoners, and after that, they set off to recruit the final member of the team - Jugo.

Sasuke's Sharingan proves to be superior against Deidara's explosives. Deidara creates one of his finest works, the C4 Karura, in order to take him down. What will Sasuke do now?

Jiraiya is now confronted by two new Pains who both possess different abilities than the one he was fighting. Just who is Pain and how many Pains are there?

Seeking to gain Sasuke's trust, Madara reveals to him the origins of Konoha. Madara and the future First Hokage founded the village long ago, but a rivalry between them would one day stem a chain of events leading to THAT night, the night that Itachi Uchiha annihilated the Uchiha Clan.

Naruto and his team, along with Hotaru and Utakata, return to Mount Katsuragi to plan their next move. Tonbei reveals a way to remove the forbidden jutsu from Hotaru's body which would result in the jutsu losing it's power. Hotaru states that if a man named Shiranami returned, the clan would be restored. Naruto decides to look for Shiranami within two days. Little do they know, the man they are looking for is actually the one after the forbidden jutsu. Meanwhile, Utakata wonders if Tsurugi spoke the truth about his master.

The Akatsuki Leader, Pain, begins his invasion of the Hidden Leaf Village. The Leaf ninja assemble to protect Naruto's whereabouts, but when Pain targets Iruka, Kakashi must face off against him.

Naruto successfully begins taking out Pain's bodies one after another, but when his Sage Mode reaches its limit, Pain attempts to take control of the battle. Is the moment of Pain's victory at hand, or does Naruto have a plan?

With Nagato's story done, Naruto tells him his answer, declaring that he won't abandon the legacy of his master, and he'll keep striving for peace no matter what pain he's put through. Nagato reflects on what Naruto says, thinking back to his final days as one of Jiraiya's students. How will Nagato ultimately respond to Naruto's answer?

After hearing the news about Akatsuki's attack on the Hidden Leaf Village, Gaara worries about Naruto's well-being. He remembers a time in the past where Team 7 was assigned to help him out with a problem, and how nobody, especially Naruto, was eager to trust him. Yet, when his life was put in danger by people he had wronged, Naruto was the first to come to his rescue.

Konohamaru's team asks Neji to talk about Naruto's heroism. Instead, Neji tells them about an incident during the Chunin exams three years prior. While Orochimaru attacked Konoha, two rogue ninja take advantage of the commotion and kidnap Hinata. Neji, Tenten, Kiba, and Akamaru rush out to save her. They're in trouble until Hiashi shows up and saves them, telling Neji that he's the beloved memory of Hiashi's younger brother. Neji realizes Naruto's speech about destiny was right; he isn't just a slave to the clan name. Konohamaru's team complains that Naruto wasn't in the story at all, and Neji cryptically answers that Naruto was the most important part.

With Team Hawk exposed, Sasuke begins to ruthlessly take down all opposing samurai. Raikage, along with Darui and Shii, track down Sasuke. The two sides engage in battle, and Suigetsu and Juugo join the fray. Which side will win this battle of overwhelming power?

Sakura ditches her team and goes alone to Sasuke's location. Meanwhile, Madara advises Sasuke to finish off Karin, but at the last second Sakura intervenes. After so long, what interaction will take place between Sasuke and Sakura?

Might Guy recalls their "visualization" training with Lee in order to avoid learning the Drunken Fist and forgetting an incident which Might Guy apologizes to the restaurant owner with humiliation. Lee, who is determined to train to be stronger than Naruto, follows Might Guy's orders and resemble animal fighting styles which represent on a restaurant menu. However they failed, until they tried on training on a moving boat. Like Guy who has seasickness, Lee also suffers from seasickness but he uses it to balance the boat which resembles exactly as the Drunken Fist fighting style. Guy lately realizes that Lee is also aware of the restaurant incident and Lee was only protecting Guy from a drunk man which causes the restaurant to be totally damaged.

Tenten remembers when she was little and how she really wanted to become like the legendary Tsunade. She finds out through hard training that she won't be capable of the strength Tsunade has. She also finds out that she won't be suitable to be a medical ninja for her poor chakra control. But at last, she discovers that she has the ability to summon ninja tools, thus creating her own style of fighting.

Sixteen years ago, Fourth Hokage Minato Namikaze and his wife Kushina are expecting their first child, much to the delight of the young couple.

The Allied Shinobi Forces’ commando unit engages with the Akatsuki in the first wave of battle.

Kankuro’s Commando Unit is cornered by Hanzo’s poison attack. Fortunately, Mifune and his Fifth Company arrive in time to provide assistance.

While training in Chakra Mode, Naruto senses the presence of the Nine Tails’ chakra seeping from Kinkaku outside. Curious to find out what’s happening, Naruto tries to leave the training room when Iruka suddenly steps in to stop him.

Tsunade and the Raikage arrive to prevent Naruto and Killer Bee from joining the battle. But the two Kage fail to convince the Jinchuriki to turn back, forcing the Raikage to use extreme force.

As Guy and Kakashi prepare to regroup their forces, they receive word that one of the units were engaged in battle with Ameyuri Ringo and decide to head to that location.

Temari leads the attack on the Third Raikage using Wind Style, but even her strongest jutsu is not enough to penetrate the Raikage’s invincible armor.

Naruto and the others finally regain their lost memories regarding Yota. Years ago, the Leaf Village kids came to befriend Yota, but the adults believed the young boy was a spy and took him away for questioning.

Kabuto attempts to bring Sasuke over to his side by pointing out that they both are fighting for the same goal: to bring down the Leaf Village. But Sasuke quickly rejects him.

Thanks to Itachi, the Reanimation Jutsu is released, and all the Reanimated Shinobi are returned to their resting places. But to everyone’s surprise, the real Madara still remains!

Obito watches in disbelief as Kakashi kills Rin. Unable to accept the harsh reality, Obito decides to carry out Madara’s dream so that he can create an ideal world where Rin still exists.

Orochimaru is forced to flee the Hidden Leaf after Third Hokage Hiruzen exposes his illegal experiments. Danzo, fearing that Orochimaru’s capture would lead to the exposure of his own involvement in the experiments, sends out one of his men to help.

Itachi Uchiha is inducted into Kakashi’s unit as the youngest member of the ANBU Black Ops. Itachi’s father, Fugaku, is pleased, thinking this will grant the Uchiha access to exclusive, top-secret Leaf intel.

Kakashi desperately tries to reach out to Obito, but his words fall on deaf ears. Obito instead accuses Kakashi of being trash, which angers Naruto, forcing him to step in and defend his Sensei.

The Senju and Uchiha clans join together to build a shinobi village and fulfill their dreams.

Team 7 is finally reunited when Naruto, Sakura and Sasuke join forces.

Obito completely absorbs the giant Ten Tails, undergoes a transformation and becomes the Ten Tails' Jinchuriki.

The Ten Tails morphs into its final form, "The Divine Tree," and attacks the shinobi, absorbing their chakra one after another.

All the Tailed Beasts are freed, and old friends Kakashi and Obito come face to face with each other. What will Obito's response be? Meanwhile, the Tailed Beasts and the Allied Shinobi Forces shift their focus onto their greatest foe, Madara Uchiha. Gaara is reunited with his former Tailed Beast, Shukaku. When Gaara asks Shukaku to lend his power to seal Madara, he refuses. Will their history of animosity prevent them from working together?

On the night before the Second Exam, the entrants gather in the cafeteria, and a brawl breaks out.

Kiba and his team are in pursuit of Hidden Grass Ninja who have stolen their scroll!

Sakura and her team continue their trek across the desert towards the goal. Their continuous battles have depleted Sakura's chakra, so they stop to rest. Just then, they encounter a puppet manipulated by a rival team from the Sand and end up being discovered.

Neji and the team come across Matsuri collapsed in the desert and find out that Gaara is in danger. Meanwhile, the chains of a mysterious priest bind Gaara and Foo.

Guy releases his Eight Inner Gates against Madara, but the Seventh Gate of Shock does not work against him!

It’s been three years since Naruto set out to train with Jiraiya, and he's just returned to the Hidden Leaf Village. Konohamaru immediately begs Naruto to teach him a new jutsu and he starts to go over the basics...but his explanations are very vague. Soon after, Naruto sets out on a mission, leaving Konohamaru to figure it out alone!

Tenten falls under the Infinite Tsukuyomi and wakes up in the Hidden Leaf Village. When Lee and Guy Sensei appear, Tenten is relieved to see that she is not alone. But her joy is short-lived, as both men act oddly and are dressed stylishly—just where has she been transported to?

Tsunade continues to read Jiraiya’s novel. Chunin- and jonin-level ninja have gone missing, and the Fourth Hokage, Minato, orders a search mission with teams of genin led by Guy and Kurenai. Kakashi’s Team 7 is also dispatched, but the hero Naruto Uzumaki, despite being the Hokage’s son, has the misfortune of being labeled a loser.

Naruto’s strength is recognized by his fellow genin, except Sasuke. But while Naruto enjoys a close relationship with his father, Sasuke’s father, Fugaku, constantly compares Sasuke with his older brother Itachi and barely pays attention to him…

Sasuke has left with Orochimaru, but Naruto is not about to give up. Determined to bring Sasuke back, he returns to the village with Shikamaru and the others. Meanwhile, Yahiko appears in the village, calling himself “Pain" and seeking revenge for the Hidden Leaf’s betrayal.

Kaguya Otsutsuki suddenly emerges from Madara’s body. She is the mother of Hagoromo, the Sage of the Six Paths who entrusted his powers to Naruto and Sasuke. Kaguya’s power is immense and instantly sends Naruto and Sasuke to an alternate dimension. Naruto and Sasuke are the only ones who can seal away Kaguya, but they can’t find a jutsu that works against her!

Chakra—whose energy connects this world to those beyond—allows Obito to leave Rin's side for a moment and appear in Kakashi’s inner psyche. Obito gives him his Magekyo Sharingan and leaves with a parting wish that Kakashi become the Sixth Hokage.